i pretty much do what you do, usually brushing away the flaking bits very gently by just dabbing a little aquaphor on the area. if it's clinging on then i don't try to pull it off, i just smooth the aquaphor over it. personally i've never made things worse by doing that so it's pretty safe if the flaking is minimal.
and HC works best when there's as little buildup as possible so it can penetrate the skin